Energy Surface For Reaction Research Articles

Theoretical study on the addition reactions of MeOH, PhOH and PhSH to silastannenes

The mechanism and potential energy surface of the addition reactions of MeOH, PhOH and PhSH to some silastannenes were investigated by using density functional theory (DFT) calculations. The influences of the number of MeOH or PhOH molecule, some substituents at Si or Sn atoms, and benzene as a solvent on the energy surface of the reactions were also explored. The obtained results indicate that most studied reactions consist of a two-step mechanism via a Lewis adduct and the initial step of the reactions is a nucleophilic or electrophilic attack of MeOH, PhOH or PhSH. The formation of SiO(S) or SnO(S) bond is prior to that of SnH or SiH bond in all studied reactions. The monomer of PhOH adds to silastannenes more readily than the corresponding dimer and trimer kinetically. The computational results explain the experimentally observed regioselectivity well.

Atmospheric gas phase chemistry of CH2═NH and HNC. A first-principles approach.

Quantum chemical methods were used to investigate the OH initiated atmospheric degradation of methanimine, CH2═NH, the major primary product in the atmospheric photo-oxidation of methylamine, CH3NH2. Energies of stationary points on potential energy surfaces of reaction were calculated using multireference perturbation theory and coupled cluster theory. The results show that hydrogen abstraction dominates over the addition route in the CH2═NH + OH reaction, and that the major primary product is HCN, while HNC and CHONH2 are minor primary products. HNC is found to react with OH exclusively via addition to the carbon atom followed by O-H scission leading to HNCO; N2O is not a product in the atmospheric photo-oxidation of HNC. Additional G4 calculations of the CH2═NH + O3 reaction show that this is too slow to be of importance at atmospheric conditions. Rate coefficients for the CH2═NH + OH and HNC + OH reactions were calculated as a function of temperature and pressure using a master equation model based on the coupled cluster theory results. The rate coefficients for OH reaction with CH2═NH and HNC at 1000 mbar and room temperature are calculated to be 3.0 × 10(-12) and 1.3 × 10(-11) cm(3) molecule(-1) s(-1), respectively. The atmospheric fate of CH2═NH is discussed and a gas phase photo-oxidation mechanism is presented.

THEORETICAL STUDY OF MECHANISM FOR THE ATMOSPHERIC REACTION CF3CHFO2 + NO

The mechanism of the reaction CF3CHFO2 + NO was investigated using ab initio and density functional theory (DFT). The optimized geometries for all stationary points on the reaction energy surface were calculated using MP2 and B3LYP methods with the aug-cc-pVDZ basis set. Single-point energy calculations were performed using the coupled cluster method with single, double and perturbative triple configurations, CCSD(T). The most important energy minima on the potential energy surface (PES) were found corresponding to two conformers of the peroxynitrite association adducts, cis- CF3CHFOONO and trans- CF3CHFOONO , and the nitrate, CF3CHFONO2 . The radical pairs ( CF3CHFO + NO2 ) and the nitrate are formed through the breaking of the peroxy bond of trans- CF3CHFOONO and the rearrangement of cis- CF3CHFOONO , respectively. The nitrate can be decomposed to carbonylated species ( CF3CHO or CF3CFO ), nitryl fluoride (NO2F), nitrous acid (HONO), and radical pairs ( CF3CHFO + NO2 ), which are of potential atmospheric importance.

ChemInform Abstract: Potential Energy Surfaces for Reactions of X Metal Atoms (X: Cu, Zn, Cd, Ga, Al, Au, or Hg) with YH4 Molecules (Y: C, Si, or Ge) and Transition Probabilities at Avoided Crossings in Some Cases

AbstractReview: ab initio studies based on quantum mechanics; 104 refs.

Potential Energy Surfaces for Reactions of X Metal Atoms (X = Cu, Zn, Cd, Ga, Al, Au, or Hg) with YH4 Molecules (Y = C, Si, or Ge) and Transition Probabilities at Avoided Crossings in Some Cases

We review ab initio studies based on quantum mechanics on the most important mechanisms of reaction leading to the C–H, Si–H, and Ge–H bond breaking of methane, silane, and germane, respectively, by a metal atom in the lowest states in symmetry: X(2nd excited state, 1st excited state and ground state) + YH4 H3XYH H + XYH3 and XH + YH3. with X = Au, Zn, Cd, Hg, Al, and G, and Y = C, Si, and Ge. Important issues considered here are (a) the role that the occupation of the d-, s-, or p-shells of the metal atom plays in the interactions with a methane or silane or germane molecule, (b) the role of either singlet or doublet excited states of metals on the reaction barriers, and (c) the role of transition probabilities for different families of reacting metals with these gases, using the H–X–Y angle as a reaction coordinate. The breaking of the Y–H bond of YH4 is useful in the production of amorphous hydrogenated films, necessary in several fields of industry.

Guided ion beam and theoretical study of the reactions of Os+ with H2, D2, and HD

Reactions of the third-row transition metal cation Os(+) with H(2), D(2), and HD to form OsH(+) (OsD(+)) were studied using a guided ion beam tandem mass spectrometer. A flow tube ion source produces Os(+) in its (6)D (6s(1)5d(6)) electronic ground state level. Corresponding state-specific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of OsH(+) and OsD(+) are analyzed to give a 0 K bond dissociation energy of D(0)(Os(+)-H) = 2.45 ± 0.10 eV. Quantum chemical calculations are performed here at several levels of theory, with B3LYP approaches generally overestimating the experimental bond energy whereas results obtained using BHLYP and CCSD(T), coupled-cluster with single, double, and perturbative triple excitations, levels show good agreement. Theory also provides the electronic structures of these species and the potential energy surfaces for reaction. Results from the reactions with HD provide insight into the reaction mechanism and indicate that Os(+) reacts via a direct reaction. We also compare this third-row transition metal system with the first-row and second-row congeners, Fe(+) and Ru(+), and find that Os(+) reacts more efficiently with dihydrogen, forming a stronger M(+)-H bond. These differences can be attributed to the lanthanide contraction and relativistic effects.

Potential energy surfaces for gas-surface reactions

A method for constructing the potential energy surface for reactions of a molecule with the surface of cleaved non-conducting crystals is reported. The method uses systematic fragmentation to express the total potential in terms of potential energy surfaces which describe reactions of relatively small molecules in the gas phase. The approach is illustrated by an application to the reaction of hydrogen atoms with a hydrogen-terminated silicon(111) surface.

Mechanism of Hydrodeoxygenation of Acrolein on a Cluster Model of MoO3

We have explored the potential energy surface for reactions of acrolein on a Mo3O9 cluster model of the MoO3 surface to investigate the thermodynamics and kinetics of hydrogenation and selective hydrodeoxygenation. In the presence of hydrogen, conversions of acrolein to allyl alcohol, 1-propanol, and propene are all thermodynamically favorable, but the selectivity is controlled kinetically to form the least favorable product, allyl alcohol. We propose a mechanism in which coordinatively unsaturated Mo sites (i.e., oxygen vacancies) selectively chemisorb acrolein. On the basis of experimental and theoretical evidence, the active phase of the catalyst is a reduced hydrogen bronze, HxMoO3−y, and surface hydroxyl sites are occupied when x is in the range 1.1−1.2. Surface hydroxyls are important for both oxygen vacancy formation and as Bronsted acids. The reaction rate is essentially controlled by protonation of the C-1 carbon of chemisorbed acrolein. Additional reaction barriers for proton donation to the C-2...

Guided ion beam and theoretical studies of the reaction of Ag+ with CS2: Gas-phase thermochemistry of AgS+ and AgCS+ and insight into spin-forbidden reactions

The gas-phase reactivity of the atomic transition metal cation, Ag(+), with CS(2) is investigated using guided-ion beam mass spectrometry. Endothermic reactions forming AgS(+) and AgCS(+) are observed but are quite inefficient. This observation is largely attributed to the stability of the closed shell Ag(+)((1)S,4d(10)) ground state, but is also influenced by the fact that the reactions producing ground state AgS(+) and AgCS(+) products are both spin forbidden. Analysis of the kinetic energy dependence of the cross sections for formation of these two products yields the 0 K bond energies of D(0)(Ag(+)-S)=1.40+/-0.12 eV and D(0)(Ag(+)-CS)=1.98+/-0.14 eV. Quantum chemical calculations are used to investigate the electronic structure of the two product ions as well as the potential energy surfaces for reaction. The primary mechanism involves oxidative addition of a CS bond to the metal cation followed by simple Ag[Single Bond]S or Ag[Single Bond]CS bond cleavage. Crossing points between the singlet and triplet surfaces are located near the transition states for bond activation. Comparison with analogous work on other late second-row transition metal cations indicates that the location of the crossing points bears directly on the efficiency of these spin-forbidden processes.

Spontaneous coal combustion producing carbon dioxide and water

Gas products from the process of coal oxidization and spontaneous combustion have been studied at different temperatures with FTI spectroscopic tests. With temperatures rising to about 30∼100 °C, water and carbon dioxide gas were formed and from about 105∼150 °C, carbon monoxide was produced. Using the DFT B3LYP method with a 6-311G basis set, the reaction system, where spontaneous combustion between coal and oxygen occurs and produces water and monoxide, has been studied, with the geometric configuration for all stagnation points on the potential reaction energy surface optimized. With a frequency analysis and an IRC method, transient formations were tested. Our results indicate that in the reaction of coal oxidization and spontaneous combustion producing carbon dioxide and water, oxygen molecules attack carbon atoms of the terminal of the propyl alcohol group on the lateral chain of benzene rings, which causes this propyl alcohol group to produce the acid (-CH 2-CH 2-COOH) group and water. This acid group continues its break up into carbon dioxide and the (-CH 2-CH 3) ethyl group. We have come to the conclusion that this water-and-carbon dioxide-production reaction is spontaneous, based on the observation of the energy released by the reaction.

Efficient Approach to Reactive Molecular Dynamics with Accurate Forces.

Density functional theory is a powerful and efficient method for calculating potential energy surfaces for chemical reactions, but its application to complex systems, such as reactions in enzymes, is often prohibitively expensive, even when high-level theory is applied only to a primary subsystem, such as an active site, and when the remaining system is treated by molecular mechanics. Here we show how the combination of multiconfiguration molecular mechanics with charge response kernels can speed up such calculations by three or more orders of magnitude. The resulting method, called electrostatically embedded multiconfiguration molecular mechanics, is illustrated by calculating the free energy of activation profile for the dehalogenation of 1,2-dichloroethane by haloalkane dehalogenase. This shows how hybrid density functionals or other high-level electronic structure methods can now be used efficiently in simulations that require extensive sampling, such as for calculating free energy profiles along a high-barrier reaction coordinate.

Reactions in the liquid phase

It is argued that a generalized Smoluchowski equation should be used to describe reactions in the liquid phase. The nature of the solutions to this equation is discussed. The reaction energy surface is partitioned into regions, defining the various species present, and solutions for each region are described. A set of master equations is used to calculate the rate constant. Application is made to a model situation where two structureless molecules react.

Kinetics of Enol Formation from Reaction of OH with Propene

Kinetics of enol generation from propene has been predicted in an effort to understand the presence of enols in flames. A potential energy surface for reaction of OH with propene was computed by CCSD(T)/cc-pVDZ//B3LYP/cc-pVTZ calculations. Rate constants of different product channels and branching ratios were then calculated using the Master Equation formulation (J. Phys. Chem. A 2006, 110, 10528). Of the two enol products, ethenol is dominant over propenol, and its pathway is also the dominant pathway for the OH + propene addition reactions to form bimolecular products. In the temperature range considered, hydrogen abstraction dominated propene + OH consumption by a branching ratio of more than 90%. Calculated rate constants of enol formation were included in the Utah Surrogate Mechanism to model the enol profile in a cyclohexane premixed flame. The extended model shows consistency with experimental data and gives 5% contribution of ethenol formation from OH + propene reaction, the rest coming from ethene + OH.

Haptic quantum chemistry

We present an implementation designed to physically experience quantum mechanical forces between reactants in chemical reactions. This allows one to screen the profile of potential energy surfaces for the study of reaction mechanisms. For this, we have developed a interface between the user and a virtual laboratory by means of a force-feedback haptic device. Potential energy surfaces of chemical reactions can be explored efficiently by rendering in the haptic device the gradients calculated with first-principles methods. The underlying potential energy surface is accurately fitted on the fly by the interpolating moving least-squares (IMLS) scheme to a grid of quantum chemical electronic energies (and geometric gradients). In addition, we introduce a new IMLS-based method to locate minimum-energy paths between two points on a potential energy surface.

A Combined Method for Determining Reaction Transition State Geometry and Energy

We found an alternative method for the derivation of transition state structure energy in chemical reactions which would be less dependent on the starting geometry of reactants by combining a mathematical tool and artificial neural networks (ANN) with conventional transition state optimization algorithms. When two reactants approach each other, every geometric structure corresponds to a system energy value. The purpose of this investigation was to collect as many energy values on the reaction energy surface as possible. By simulating the energy surface using the geometric parameters as independent variables, the first order saddle point in the energy surface corresponding to the transition state structure was derived. The nucleophilic attack step of a classical Aldol reaction was studied using acetaldehyde anion and formaldehyde as reactants. The intrinsic reaction coordinate (IRC) path calculation started with 3 different sets of starting reactant geometries and 96 points on the reaction energy surface were derived. The energy surface was simulated using ANN. Cross-validation was applied to evaluate the result and avoided a possible overfitting of the ANN.

An Effective Hamiltonian Molecular Orbital-Valence Bond (MOVB) Approach for Chemical Reactions Applied to the Nucleophilic Substitution Reaction of Hydrosulfide Ion and Chloromethane.

An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix element H(12) such that the computed energy of reaction from the EH-MOVB method is in agreement with the target value. The scaling factor is very close to unity, resulting in minimal alteration of the potential energy surface of the original MOVB model. Furthermore, the relative energy between the reactant and product diabatic states in the EH-MOVB method can be improved to match the experimental energy of reaction. A key ingredient in the EH-MOVB theory is that the off-diagonal matrix elements are functions of all degrees of freedom of the system and the overlap matrix is explicitly evaluated. The EH-MOVB method has been applied to the nucleophilic substitution reaction between hydrosulfide and chloromethane to illustrate the methodology and the results were matched to reproduce the results from ab initio valence bond self-consistent valence bond (VBSCF) calculations. The diabatic coupling (the off-diagonal matrix element in the generalized secular equation) has small variations along the minimum energy reaction path in the EH-MOVB model, whereas it shows a maximum value at the transition state and has nearly zero values in the regions of the ion-dipole complexes from VBSCF calculations. The difference in the diabatic coupling stabilization is attributed to the large overlap integral in the computationally efficient MOVB method.

Reactions of Hf +, Ta +, and W + with O 2 and CO: Metal carbide and metal oxide cation bond energies

The reactions of Hf +, Ta +, and W + with O 2 and CO are studied as a function of translational energy in a guided ion beam tandem mass spectrometer. All three reactions with O 2 form diatomic metal oxide cations in exothermic reactions that occur at the collision rate. In the CO systems, formation of both diatomic metal oxide and metal carbide cations is observed to be endothermic. The energy-dependent cross sections in the latter systems are interpreted to give 0 K bond energies (in eV) of D 0(HfC +) = 3.19 ± 0.03, D 0(TaC +) = 3.79 ± 0.04, D 0(WC +) = 4.76 ± 0.09, D 0(HfO +) = 6.91 ± 0.11, D 0(TaO +) = 7.10 ± 0.12, and D 0(WO +) = 6.77 ± 0.07. The present experimental values for TaO + and WC + agree well with literature thermochemistry, those for HfO + and WO + refine the available literature bond energies, and those for HfC + and TaC + are the first measurements available. The nature of the bonding in MO + and MC + is discussed and compared for these three metal ions and analyzed using theoretical calculations at a B3LYP/HW+/6-311+G(3df) level of theory. Bond energies for all MO + and MC + species are calculated using geometries calculated at this level and single point energies determined at B3LYP, CCSD, CCSD(T), QCISD, and QCISD(T) levels of theory with the same basis set. Reasonable agreement between the theoretical and experimental bond energies for the three metal oxide and three metal carbide cations is found. Potential energy surfaces for reaction of the metal cations with CO are also calculated at the B3LYP level of theory and reveal additional information about the reaction mechanisms.

A parallel distributed data CPHF algorithm for analytic Hessians

One of the most commonly used means to characterize potential energy surfaces of reactions and chemical systems is the Hessian calculation, whose analytic evaluation is computationally and memory demanding. A new scalable distributed data analytic Hessian algorithm is presented. Features of the distributed data parallel coupled perturbed Hartree-Fock (CPHF) are (a) columns of density-like and Fock-like matrices are distributed among processors, (b) an efficient static load balancing scheme achieves good work load distribution among the processors, (c) network communication time is minimized, and (d) numerous performance improvements in analytic Hessian steps are made. As a result, the new code has good performance which is demonstrated on large biological systems.

NMR studies of double proton transfer in hydrogen bonded cyclic N,N′-diarylformamidine dimers: conformational control, kinetic HH/HD/DD isotope effects and tunneling

Using dynamic NMR spectroscopy, the kinetics of the degenerate double proton transfer in cyclic dimers of polycrystalline (15)N,(15)N'-di-(4-bromophenyl)-formamidine (DBrFA) have been studied including the kinetic HH/HD/DD isotope effects in a wide temperature range. This transfer is controlled by intermolecular interactions, which in turn are controlled by the molecular conformation and hence the molecular structure. At low temperatures, rate constants were determined by line shape analysis of (15)N NMR spectra obtained using cross-polarization (CP) and magic angle spinning (MAS). At higher temperatures, in the microsecond time scale, rate constants and kinetic isotope effects were obtained by a combination of longitudinal (15)N and (2)H relaxation measurements. (15)N CPMAS line shape analysis was also employed to study the non-degenerate double proton transfer of polycrystalline (15)N,(15)N'-diphenyl-formamidine (DPFA). The kinetic results are in excellent agreement with the kinetics of DPFA and (15)N,(15)N'-di-(4-fluorophenyl)-formamidine (DFFA) studied previously for solutions in tetrahydrofuran. Two large HH/HD and HD/DD isotope effects are observed in the whole temperature range which indicates a concerted double proton transfer mechanism in the domain of the reaction energy surface. The Arrhenius curves are non-linear indicating a tunneling mechanism. Arrhenius curve simulations were performed using the Bell-Limbach tunneling model. The role of the phenyl group conformation and hydrogen bond compression on the barrier of the proton transfer is discussed.

Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

The multiconfiguration molecular mechanics (MCMM) method is a general algorithm for generating potential energy surfaces for chemical reactions by fitting high-level electronic structure data with the help of molecular mechanical (MM) potentials. It was previously developed as an extension of standard MM to reactive systems by inclusion of multidimensional resonance interactions between MM configurations corresponding to specific valence bonding patterns, with the resonance matrix element obtained from quantum mechanical (QM) electronic structure calculations. In particular, the resonance matrix element is obtained by multidimensional interpolation employing a finite number of geometries at which electronic-structure calculations of the energy, gradient, and Hessian are carried out. In this paper, we present a strategy for combining MCMM with hybrid quantum mechanical molecular mechanical (QM/MM) methods. In the new scheme, electronic-structure information for obtaining the resonance integral is obtained by means of hybrid QM/MM calculations instead of fully QM calculations. As such, the new strategy can be applied to the studies of very large reactive systems. The new MCMM scheme is tested for two hydrogen-transfer reactions. Very encouraging convergence is obtained for rate constants including tunneling, suggesting that the new MCMM method, called QM/MM-MCMM, is a very general, stable, and efficient procedure for generating potential energy surfaces for large reactive systems. The results are found to converge well with respect to the number of Hessians. The results are also compared to calculations in which the resonance integral data are obtained by pure QM, and this illustrates the sensitivity of reaction rate calculations to the treatment of the QM-MM border. For the smaller of the two systems, comparison is also made to direct dynamics calculations in which the potential energies are computed quantum mechanically on the fly.